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4,391 results for “cryptic”

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dryad36/100

Can cryptic female choice prevent invasive hybridization in external fertilizing fish?

Polyandrous mating systems result in females mating with multiple males, generating opportunities for strong pre-mating and post-mating sexual selection. Polyandry also creates the potential for unintended matings and subsequent sperm competition with hybridizing species. Cryptic female choice allows females to bias paternity towards preferred males under sperm competition and may include conspecific sperm preference when under hybridization risk. The potential for hybridization becomes particularly important in context of invasive species that can novelly hybridize with natives, and by definition, have evolved allopatrically. We provide the first examination of conspecific sperm preference in a system of three species with the potential to hybridize: North American native Atlantic salmon (Salmo salar) and brook char (Salvelinus fontinalis), and invasive brown trout (Salmo trutta) from Europe. Using naturalized populations on the island of Newfoundland, we measured changes in sperm swimming performance, a known predictor of paternity, to determine the degree of modification in sperm swimming to female cues related to conspecific sperm preference. Compared to water alone, female ovarian fluid, in general, had a pronounced effect and changed sperm motility (by a mean of 53%) and swimming velocity (mean 30%), but not linearity (mean 6%). However, patterns in the degree of modification suggest there is no conspecific sperm preference in the North American populations. Furthermore, female cues from both native species tended to boost the sperm of invasive males more than their own. We conclude that cryptic female choice via ovarian fluid mediated sperm swimming modification is too weak in this system to prevent invasive hybridization and is likely insufficient to promote or maintain reproductive isolation among the native North American species.

opencc-zeroJul 2023View details →

dryad36/100

Rapid sperm length divergence in a polygynandrous passerine: a mechanism of cryptic speciation?

When populations become geographically isolated, they begin to diverge in various traits and at variable rates. The dynamics of such trait divergences are relevant for understanding evolutionary processes such as local adaptation and speciation. Here we examine divergences in sperm and body structures in a polygynandrous songbird, the alpine accentor (Prunella collaris) between two allopatric high-altitude populations, in Morocco and Spain. The populations diverged around 82,000 years ago, as estimated with a coalescence-based phylogenetic analysis of genome-wide single nucleotide polymorphisms. We found that birds in the two areas had non-overlapping sperm lengths. This suggests adaptation to divergent female reproductive tract environments. Sperm length also showed an exceptionally low coefficient of among-male variation, a signal of strong stabilizing selection imposed by sperm competition. The evolutionary rate of sperm length was almost twice the rates for the most divergent morphological traits, and more than three times higher than expected from literature data over a similar generational timescale. This rapid evolution of a key reproductive trait has implications for reproductive isolation and ultimately for speciation. Strong selection for different sperm length optima in allopatry predicts conspecific sperm precedence and disruptive selection in sympatry, hence a possible postcopulatory prezygotic barrier to gene flow.

opencc-zeroAug 2023View details →

zenodo36/100

A new cryptic species of terrestrial breeding frog of the Pristimantis danae Group (Anura: Strabomantidae) from montane forests in Ayacucho, Peru.

File 1: Genetic distances rRNA 16S (p-uncorrected genetic distances) in Mega11. Excel file. For a description of a new species (Pristimantis similaris) in the publication Herrera-Alva et al. 2023. File 2: Alignment of four concatenated genes 16S rRNA, COI, RAG1, and TYR. Fasta file. For a description of a new species (Pristimantis similaris) in the publication Herrera-Alva et al. 2023.

opencc-by-4.0Dec 2022View details →

dryad36/100

Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid

Most insects harbor influential, yet non-essential heritable microbes in their hemocoel. Communities of these symbionts exhibit low diversity. But their frequent multi-species nature raises intriguing questions on roles for symbiont-symbiont synergies in host adaptation, and on the stability of the symbiont communities, themselves. In this study, we build on knowledge of species-defined symbiont community structure across United States populations of the pea aphid, Acyrthosiphon pisum. Through extensive symbiont genotyping, we show that pea aphids' microbiomes can be more precisely defined at the symbiont strain level, with strain variability shaping ~5 out of 9 previously reported co-infection trends. Field data provide a mixture of evidence for symbiont-symbiont synergies, and symbiont hitchhiking, revealing causes and consequences of these co-infection trends. To test whether within-host metabolic interactions predict common versus rare strain-defined communities, we leveraged the high relatedness of our dominant, community-defined symbiont strains vs. twelve pea aphid-derived Gammaproteobacteria with sequenced genomes. Genomic inference, using metabolic complementarity indices, revealed high potential for cooperation among one pair of symbionts – Serratia symbiotica and Rickettsiella viridis. Applying the expansion network algorithm, through additional use of pea aphid and obligate Buchnera symbiont genomes, Serratia and Rickettsiella emerged as the only symbiont community requiring both parties to expand holobiont metabolism. Through their joint expansion of the biotin biosynthesis pathway, these symbionts may span missing gaps within a multi-party mutualism, within their nutrient-limited phloem-feeding hosts. Recent, complementary gene inactivation, within the biotin pathways of Serratia and Rickettsiella, raise further questions on the origins of mutualisms and host-symbiont interdependencies.

opencc-zeroAug 2023View details →

dryad36/100

Spatiotemporal organization of cryptic North American Culex species along an urbanization gradient

Landscape heterogeneity creates diverse habitat and resources for mosquito vectors of disease. A consequence may be varied distribution and abundance of vector species over space and time dependent on niche requirements. We tested the hypothesis that landscape heterogeneity driven by urbanization influences the distribution and relative abundance of Culex pipiens , Cx. restuans, and Cx. quinquefasciatus, three vectors of West Nile virus (WNv) in the eastern North American landscape. We collected 9,803 cryptic Culex from urban, suburban, and rural sites in metropolitan Washington, District of Columbia, during the months of June-October, 2019-2021. In 2021, we also collected mosquitoes in April and May to measure early-season abundance and distribution. Molecular techniques were used to identify a subset of collected Culex to species (n = 2,461). Ecological correlates of the spatiotemporal distribution of these cryptic Culex were examined using constrained and unconstrained ordination. Seasonality was not associated with Culex community composition in June-October over three years but introducing April and May data revealed seasonal shifts in community composition in the final year of our study. Culex pipiens were dominant across site types, while Cx. quinquefasciatus were associated with urban environments, and Cx. restuans were associated with rural and suburban sites. All three species rarely coexisted. Synthesis and applications: Our work demonstrates that human-mediated land-use changes influence the distribution and relative abundance of Culex vectors of WNv, even on fine geospatial scales. Site classification, percent impervious surface, distance to city center, and longitude predicted Culex community composition. We documented active Culex months before vector surveillance typically commences in this region, with Culex restuans being most abundant during April and May. Active suppression of Cx. restuans in April and May could reduce early enzootic transmission, delay the seasonal spread of WNv, and thereby reduce overall WNv burden. By June, the highest risk of epizootic spillover of WNv to human hosts may be in suburban areas with high human population density and mixed Culex assemblages that can transmit WNv between birds and humans. Focusing management efforts there may further reduce human disease burden.

opencc-zeroSep 2023View details →

dryad36/100

Data from: Remote homolog detection places insect chemoreceptors in a cryptic protein superfamily spanning the tree of life

Many proteins exist in the so-called "twilight zone" of sequence alignment, where low pairwise sequence identity makes it difficult to determine homology and phylogeny. As protein tertiary structure is often more conserved, recent advances in ab initio protein folding have made structure-based identification of putative homologs feasible. However, structural screening and phylogenetics are in their infancy, particularly for twilight zone proteins. We present a pipeline for the identification and characterization of distant homologs, and apply it to 7-transmembrane domain ion channels (7TMICs), a protein group founded by insect Odorant and Gustatory receptors. Previous sequence and limited structure-based searches identified putatively-related proteins, mainly in other animals and plants. However, very few 7TMICs have been identified in non-animal, non-plant taxa. Moreover, these proteins' remarkable sequence dissimilarity made it uncertain if disparate 7TMIC types (Gr/Or, Grl, GRL, DUF3537, PHTF and GrlHz) are homologous or convergent, leaving their evolutionary history unresolved. Our pipeline identified thousands of new 7TMICs in archaea, bacteria and unicellular eukaryotes. Using graph-based analyses and protein language models to extract family-wide signatures, we demonstrate that 7TMICs have structure and sequence similarity, supporting homology. Through sequence and structure-based phylogenetics, we classify eukaryotic 7TMICs into two families (Class-A and Class-B), which are the result of a gene duplication predating the split(s) leading to Amorphea (animals, fungi and allies) and Diaphoretickes (plants and allies). Our work reveals 7TMICs as a cryptic superfamily with origins close to the evolution of cellular life. More generally, this study serves as a methodological proof of principle for the identification of extremely distant protein homologs.

opencc-zeroSep 2023View details →

dryad36/100

Genomic divergence and introgression between cryptic species of a widespread North American songbird

Analysis of genomic variation among related populations can sometimes reveal distinct species that were previously undescribed due to similar morphological appearances, and close examination of such cases can provide much insight regarding speciation. Genomic data can also reveal the role of reticulated evolution in differentiation and speciation. White-breasted nuthatches (Sitta carolinensis) are widely distributed North American songbirds that are currently classified as a single species but have been suspected to represent a case of cryptic speciation. Previous genetic analyses suggested four divergent groups, but it was unclear whether these represented multiple reproductively isolated species. Using extensive genomic sampling of over 350 white-breasted nuthatches from across North America and a new chromosome-level reference genome, we asked if white-breasted nuthatches are comprised of multiple species and whether introgression has occurred between divergent populations. Genomic variation of over 300,000 loci revealed four highly differentiated populations (Pacific, n = 45; Eastern, n = 23; Rocky Mountains North, n = 138; and Rocky Mountains South, n = 150) with geographic ranges that are adjacent. We observed a moderate degree of admixture between Rocky Mountain populations but only a small number of hybrids between the Rockies and the Eastern population. The rarity of hybrids together with high levels of differentiation between populations is supportive of populations having some level of reproductive isolation. Between populations, we show evidence for introgression from a divergent ghost lineage of white-breasted nuthatches into the Rocky Mountains South population, which is otherwise closely related to Rocky Mountains North. We conclude that white-breasted nuthatches are best considered at least 3 species and that ghost lineage introgression has contributed to differentiation between the two Rocky Mountain populations. White-breasted nuthatches provide a dramatic case of morphological similarity despite high genomic differentiation, and the varying levels of reproductive isolation among the four groups provide an example of the speciation continuum.

opencc-zeroDec 2022View details →

dryad36/100

Hetaerina SNPs data for: Genomic differentiation and niche divergence in the Hetaerina americana (Odonata) cryptic species complex

The evolution of reproductive barriers, that is, the speciation process, implies the limitation of gene flow between populations. Different patterns of genomic differentiation throughout the speciation continuum may provide insights into the causal evolutionary forces of species divergence. In this study, we analyzed a cryptic species complex of the genus Hetaerina (Odonata). This complex includes H. americana and H. calverti; however, in H. americana, two highly differentiated genetic groups have been previously detected, which, we hypothesize, may correspond to different species with low morphological variation. We obtained single nucleotide polymorphism (SNP) data for 90 individuals belonging to the different taxa in the complex and carried out differentiation tests to identify genetic isolation. The results from STRUCTURE and discriminant analysis of principal components (DAPC), based on almost 5,000 SNPs, confirmed the presence of three highly differentiated taxa. Also, we found FST values above 0.5 in pairwise comparisons, which indicates a considerable degree of genetic isolation among the suggested species. We also found low climatic niche overlap among all taxa, suggesting that each group occurs at specific conditions of temperature, precipitation and elevation. We propose that H. americana comprises two cryptic species, which may be reproductively isolated by ecological barriers related to niche divergence, since the morphological variation is minimal and, therefore, mechanical barriers are probably less effective compared to other related species such as H. calverti.

opencc-zeroOct 2023View details →

zenodo36/100

Data and code from Pierson et al. "Revisiting a cryptic species complex: interspecific gene flow among woodland salamanders in the Blue Ridge Mountains of northern Georgia"

ABSTRACT The complex topography of mountainous landscapes can create biogeographic barriers and promote allopatric speciation—even among morphologically cryptic species. However, these biogeographic barriers are rarely permanent, and secondary contact between previously independently evolving populations may result in hybridization and introgression. Here, we use genome-wide SNP data to reexamine a classic example of cryptic species in the Appalachian Mountains: the slimy salamander (Plethodon glutinosus) species complex. This group of morphologically similar terrestrial salamanders includes 14 species with parapatric distributions across the eastern United States. In this study, we focused on the Chattahoochee Slimy Salamander in northern Georgia and used a series of complementary phylogenomic and population genomic analyses to evaluate spatial genetic structure within this species and demonstrate admixture with at least four other species of parapatric woodland salamanders. Our results highlight the utility of genomic data in clarifying species boundaries and underscore the difficulty of species delimitation in organisms with complex evolutionary histories.

opencc-by-4.0Jul 2023View details →

dryad36/100